"Phylogenetic data analysis using R"
Delivered by Dr. Emmanuel Paradis
www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/
This course will run from 28th January - 2nd February 2018 at SCENE
field station, Loch Lomond, Glasgow.
The main objectives of the course are to teach the theoretical bases of
phylogenetic analysis, and to give the ability to initiate a
phylogenetic analysis starting from the files of molecular sequences
until the interpretation of the results and the graphics. The
introduction will cover a brief historical background and an overview of
the different methods of phylogenetic inference. Different kinds of data
will be considered, but with a special emphasis on DNA sequences. The
software used will be based on R and several specialized packages
(particularly ape and phangorn). Other software will be used (e.g.,
MUSCLE or Clustal) called from R. Overall, the course will cover almost
all aspects of phylogenetic inference from reading/downloading the data
to plotting the results. This course is intended for PhD and
postgraduate students, researchers and engineers in evolutionary
biology, systematics, population genetics, ecology, conservation.
Course content is as follows
Day 1
• Refresher on R: data structures, data manipulation with the indexing
system, scripts, using the help system.
• Introduction to phylogenetic inference.
• Basics on phylogenetic data (sequences, alignments, trees, networks,
“splits”) and other data in R.
• Reading / writing data from files or from internet.
• Matching data. Manipulating labels. Subsetting data.
• Main package: ape.
Day 2
• Plotting and annotating trees.
• Theory of sequence alignment. Comparing alignments. Graphical
analyses of alignments.
• Main packages: ape (with MUSCLE and Clustal).
Day 3
• Theory and methods of phylogeny reconstruction.
• Parsimony methods.
• Evolutionary distances.
• Distance-based methods: General principles and the main methods (NJ,
BIONJ, FastME, MVR).
• Methods for incomplete distances matrices (NJ*, BIONJ*, MVR*).
Methods for combining several matrices (SDM).
• Main packages: ape, phangorn.
Day 4
• Theory of maximum likelihood estimation.
• Application to phylogeny reconstruction.
• Substitution models.
• Tree space and topology estimation.
• Main packages: ape, phangorn.
Day 5
• Tree comparison, consensus methods.
• Topological space and distances.
• Bootstrap.
• Bayesian methods.
Please email any inquiries to oliverhoo...@prstatistics.com or visit our
website www.prstatistics.com
Please feel free to distribute this material anywhere you feel is
suitable
PRstatistics upcoming courses - email for details
oliverhoo...@prstatistics.com for details
1. META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES
#METR01
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena
Kulinskaya
http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/
2. SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James
Grecian
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/
3. ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/
4. GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
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5. STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY
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23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
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6. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
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7. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt
Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/
8. ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay,
Dr. Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/
9. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/
10. PHYLOGENETIC DATA ANALYSIS USING R #PHYL
28th Jan – Feb 2nd, Scotland, Dr. Emmanuel Paradis
https://www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/
11. ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
19th – 23rd February 2018, Wales, Dr Luca Borger, Dr. John Fieberg
12. GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael
Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/
13. FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND
COMPUTATION #FEER
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars
Götzenberger, Dr. Carlos Carmona
http://www.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/
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8th – 12th July 2018, Scotland, Prof David Warton
15. ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R
#MVSP
Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be
confirmed
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Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be
confirmed
17. NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed
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Prof. Subhash Lele, Dr. Peter Solymos - Date and location to be
confirmed
19. TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
Dr. Andrew Parnell - Date and location to be confirmed
------------------------------------------------------------------------------------------
PRinformatics upcoming courses - email for details
oliverhoo...@prinformaticss.com for details
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3. INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS #IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
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4. DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP
11th – 15th December 2017, Wales, Dr. Martin Jones
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5. EUKARYOTIC METABARCODING
23rd – 27th July 2018, Scotland, Dr. Owen Wangensteen
http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/
6. CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR
EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
Dr. Aline Quadros Date and location to be confirmed
7. BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB
Dr. Nic Blouin, Dr. Ian Misner Date and location to be confirmed
--
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
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prstatistics.com/organiser/oliver-hooker/
3/1, 128 Brunswick Street
Glasgow
G1 1TF
+44 (0) 7966500340
--
Oliver Hooker PhD.
PR statistics
2017 publications -
Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.
The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/
6 Hope Park Crescent
Edinburgh
EH8 9NA
+44 (0) 7966500340
_______________________________________________
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